.. _citing-sct: Citing SCT ########## If you use SCT in your research or as part of your developments, please always cite the `main reference`_. If you use specific tools such as ``sct_deepseg_sc`` or the ``PAM50`` template, please also cite the specific articles listed in `specific references`_. Main Reference -------------- - `De Leener B, Levy S, Dupont SM, Fonov VS, Stikov N, Louis Collins D, Callot V, Cohen-Adad J. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data. Neuroimage 2017. `__ .. code-block:: none @article{DeLeener201724, title = "SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord \{MRI\} data ", journal = "NeuroImage ", volume = "145, Part A", number = "", pages = "24 - 43", year = "2017", note = "", issn = "1053-8119", doi = "https://doi.org/10.1016/j.neuroimage.2016.10.009", url = "https://www.sciencedirect.com/science/article/pii/S1053811916305560", author = "Benjamin De Leener and Simon Lévy and Sara M. Dupont and Vladimir S. Fonov and Nikola Stikov and D. Louis Collins and Virginie Callot and Julien Cohen-Adad", keywords = "Spinal cord", keywords = "MRI", keywords = "Software", keywords = "Template", keywords = "Atlas", keywords = "Open-source ", } Specific References ------------------- Command Line Tools ^^^^^^^^^^^^^^^^^^ The table below provides individual references for novel methods used in SCT's :ref:`command-line-tools`. .. note:: If you are using white matter/grey matter segmentation tools (``sct_deepseg_gm``/``sct_deepseg``) and registration tools (``sct_register_to_template``/``sct_register_multimodal``) together as part of a pipeline, please also consider this reference: `Dupont SM, De Leener B, Taso M, Le Troter A, Stikov N, Callot V, Cohen-Adad J. Fully-integrated framework for the segmentation and registration of the spinal cord white and gray matter. Neuroimage 2017 `__ .. list-table:: :widths: 20 80 :header-rows: 1 * - Command line script - References * - ``sct_deepseg_gm`` - `Perone et al. Spinal cord gray matter segmentation using deep dilated convolutions. Sci Rep 2018 `__ * - ``sct_deepseg_lesion`` - `Gros et al. Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks. Neuroimage 2019 `__ * - ``sct_deepseg_sc`` - `Gros et al. Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks. Neuroimage 2019 `__ * - ``sct_get_centerline`` - `Gros et al. Automatic spinal cord localization, robust to MRI contrasts using global curve optimization. Med Image Anal 2018 `__ * - ``sct_label_vertebrae`` - `Ullmann et al. Automatic labeling of vertebral levels using a robust template-based approach. Int J Biomed Imaging 2014 `__ * - ``sct_process_segmentation -pmj`` - `Bédard S, Cohen-Adad J. Automatic measure and normalization of spinal cord cross-sectional area using the pontomedullary junction. Frontiers in Neuroimaging 2022 `__ * - ``sct_process_segmentation -normalize`` - `Bédard S, Cohen-Adad J. Automatic measure and normalization of spinal cord cross-sectional area using the pontomedullary junction. Frontiers in Neuroimaging 2022 `__ * - ``sct_propseg`` - `De Leener et al. Robust, accurate and fast automatic segmentation of the spinal cord. Neuroimage 2014 `__ * - ``sct_propseg -CSF`` - `De Leener et al. Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling. IEEE Transactions on Medical Imaging 2015 `__ * - ``sct_register_multimodal`` - `De Leener B, Fonov VS, Louis Collins D, Callot V, Stikov N, Cohen-Adad J. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space. Neuroimage 2017. `__ * - ``sct_register_multimodal --param algo=slicereg`` - `Cohen-Adad et al. Slice-by-slice regularized registration for spinal cord MRI: SliceReg. Proc ISMRM 2015 `__ * - ``sct_register_to_template`` - `De Leener B, Fonov VS, Louis Collins D, Callot V, Stikov N, Cohen-Adad J. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space. Neuroimage 2017. `__ * - ``sct_register_to_template --param algo=slicereg`` - `Cohen-Adad et al. Slice-by-slice regularized registration for spinal cord MRI: SliceReg. Proc ISMRM 2015 `__ * - ``sct_straighten_spinalcord`` - `De Leener B et al. Topologically-preserving straightening of spinal cord MRI. J Magn Reson Imaging 2017 `__ Template and Atlas ^^^^^^^^^^^^^^^^^^ The table below provides references relevant to the :ref:`pam50` used by SCT, including a reference for the template itself, as well as earlier works that the template builds on. .. list-table:: :widths: 20 80 :header-rows: 1 * - Template/atlas - References * - PAM50 template - `De Leener B, Fonov VS, Louis Collins D, Callot V, Stikov N, Cohen-Adad J. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space. Neuroimage 2018. `__ * - MNI-Poly-AMU template - `Fonov et al. Framework for integrated MRI average of the spinal cord white and gray matter: The MNI-Poly-AMU template. Neuroimage 2014. `__ * - White matter atlas - `Lévy et al. White matter atlas of the human spinal cord with estimation of partial volume effect. Neuroimage 2015 `__ * - Probabilistic atlas (AMU40) - `Taso et al. A reliable spatially normalized template of the human spinal cord–Applications to automated white matter/gray matter segmentation and tensor-based morphometry (TBM) mapping of gray matter alterations occurring with age. Neuroimage 2015 `__ * - Spinal levels - `Cadotte DW, Cadotte A, Cohen-Adad J, Fleet D, Livne M, Wilson JR, Mikulis D, Nugaeva N, Fehlings MG. Characterizing the location of spinal and vertebral levels in the human cervical spinal cord. AJNR Am J Neuroradiol, 2015, 36(4):803-810. `_